Flu season is once again around the corner and many South Africans will be turning to their trusted dose of antibiotics to resolve the outbreak as effectively as possible. Despite this ongoing routine, South Africa is facing a huge problem. A study, which was led by Julia Gasson of the Western Cape Department of Health, has revealed that local clinics are ignoring the guidelines on prescribing those antibiotics, and formal procedures are followed only 45% of the time. Another global study by the Center for Disease Dynamics, Economics & Policy (CDDEP), Princeton University, ETH Zurich and the University of Antwerp analysed human antibiotic consumption in 76 countries and found it has increased worldwide from 11.3 to 15.7 defined daily doses (DDDs) per 1,000 inhabitants per day between 2000 and 2015.
The results of these actions are far-reaching. Antibiotics have begun to lose their effectiveness and we are developing a resistance to them. And the problem is more complicated than we had first thought. In one case, it was found that antibiotic-resistant patients with infections such as E. coli and Klebsiella pneumonia had contracted a specific gene that had its origins on Chinese pig farms.
A crucial step in combatting antibiotic resistance lies in technological evolution
As a solution, scientists are now looking towards the field of bacterial genomics to tackle the global issue of antibiotic resistance. Genomics refers to the branch of molecular biology concerned with the structure, function, evolution, and mapping of our genes. This process can provide clarity around resistance mechanisms and even the evolution of various strains of disease. Today the process of genomics has also become highly automated, which has been greatly accelerated through a combination of parallel processing and the advancement in data management processes.
Due these advancements, we are now entering a world of personalised medicine, whereby individual patients can be sequenced and comparative genomic analysis can provide vital information around the progression of resistant strains of disease. Within this context, technology plays a pivotal role in allowing bioinformaticians to work with and transfer data to clinicians in an efficient and timely manner.
NetApp is assisting to achieve this through the ONTAP Cloud storage software, which allows for the protection of genomic data whilst adding the flexibility to simplify the use of public cloud. We are currently seeing this process in action through our work with PetaGene – a team which originated from Cambridge University PHDs who required a novel approach to the problem of storing data associated genomics. Additionally, we are deploying the new and improved NetApp StorageGRID which now automates tamper proof retention of critical personal data. With an increased focus on data analytics, StorageGRID customers retain and manage an unlimited amount of rich media, which is particularly useful for the field of genomics.
The key benefits of applying technology to scientific research
Unlike generic data reduction techniques, there are a few key benefits of applying the process of data management to the pursuit of tackling antibiotic resistance:
- Increased collaborative efficiency, with smaller more portable files transferable over the NetApp data fabric
- Use less storage capacity and lower costs
- Leverage the flexibility of the cloud. With the NetApp data fabric, files can be seamlessly and securely moved to and from the cloud
- Maintain interoperability with existing workflows and formats
The field of genomics, underpinned by efficient data management, is the way forward in combatting the global issue of antibiotic resistance. This, of course, needs to be coupled with the necessary behavioural changes where prescription guidelines are followed to the tee. Within South Africa, a country marred by drug-resistant infectious diseases ranging from HIV through to malaria, the need to simplify collaboration in genomics with improved data management has never been more crucial.
By Morne Bekker, country manager at NetApp South Africa